Freesurfer June 2014

freesurfer@nmr.mgh.harvard.edu

155 participants
234 discussions

NIH Staff Scientist Position available, Bethesda, MD, USA
by Thomas, Adam (NIH/NIMH) [E] 30 Jul '14

30 Jul '14

Posted on behalf of the CPB: Department of Health and Human Services (DHHS) National Institutes of Health (NIH) National Institute of Mental Health (NIMH) Division of Intramural Research Programs (DIRP) Section on Childhood Neuropsychiatric Disorders (SCND) Child Psychiatry Branch (CPB) Staff Scientist The Child Psychiatry Branch, in Bethesda, Maryland, is recruiting applicants for a Staff Scientist position. As a Staff Scientist, the primary duties will include conducting statistical analyses on clinical, neurobiological and treatment studies carried out in the Branch. This includes but is not limited to tasks such as maintaining the appropriate data sets, clearly conveying statistical results and methods both orally and in writing, reviewing and writing statistical content for manuscripts prior to submission, and working closely with and providing statistical support for all Branch members. The Staff Scientist position entails 25% time allotted to pursuing individual research interests. The Child Psychiatry Branch is a highly productive and collaborative group with a rich, multimodal dataset that seeks to understand neurodevelopmental disorders, with a focus on childhood-onset schizophrenia. There is a strong scientific and statistical computing core facility in existence, which can benefit this work. For more information about the Child Psychiatry Branch, please utilize the following link: http://www.nimh.nih.gov/labs-at-nimh/research-areas/clinics-and-labs/chp/in dex.shtml Interested candidates must have five years post-doctoral experience. Applicants should have a strong background in statistics and programming/computer science, as well as interests and experience in neuroimaging and behavioral research. The recruit should be adept at writing his/her own code to clean, organize, analyze, and visualize data. Unix and python programming skills are also preferable. In addition some highly desirable skills include: experience analyzing structural MRI, functional MRI and/or MEG data; a solid foundation in multivariate statistics (e.g., cluster analysis, principal components analysis, independent components analysis), and a background in longitudinal data analysis (e.g., mixed model regression/hierarchical linear modeling); proficiency in statistical programs such as R and MATLAB and visualization methods. SALARY RANGE: Salary is commensurate with experience and accomplishments. BENEFITS: The federal government offers a comprehensive benefits package including vacation, sick leave, holidays, life insurance, health benefits, and participation in the Federal Employees Retirement System. For more information go to new employee benefits at the NIH (http://hr.od.nih.gov/Benefits/permanentemployee.htm) and other employee benefits information (http://tiny.cc/saVcr) Interested applicants should send their CV and cover letter to Dr. Judith Rapoport, NIMH, 10 Center Drive, Bldg. 10, Rm. 3N202 (MSC-1600), Bethesda, MD 20892 USA, or by email: rapoporj(a)mail.nih.gov<mailto:rapoporj@mail.nih.gov> SUBMISSION DEADLINE: June 1, 2014 NIH and DHHS are Equal Opportunity Employers.

1 1

lgi for longitudinal scans
by Anna Jonsson 23 Jul '14

23 Jul '14

Dear group, If I want conduct gyrification analyses on the long runs that have been through the longitudinal stream, do I just perform the "normal" baseline command on the .long data? thank you, kind wishes Anna

2 5

Re: [Freesurfer] recon-all ERROR, no idea why
by Remy Wahnoun 18 Jul '14

18 Jul '14

Thanks Douglas, I definitely appreciate your help. Here is what it Spit out, *Rémy Wahnoun, PhD* Biomedical Research Group Manager Barrow Neurological Institute at Phoenix Children's Hospital Adjunct Faculty, Arizona State University *www.NeuralControl.net <http://www.neuralcontrol.net/>* set echo = 1 ; set debug = 1 ; set debug = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 11 != 0 ) set flag = $argv[1] ; shift ; set flag = --n shift switch ( $flag ) switch ( --n ) if ( $#argv == 0 ) goto arg1err ; if ( 10 == 0 ) goto arg1err set nIters = $argv[1] ; shift ; set nIters = 1 shift breaksw breaksw end end while ( $#argv != 0 ) while ( 9 != 0 ) set flag = $argv[1] ; shift ; set flag = --proto-iters shift switch ( $flag ) switch ( --proto-iters ) if ( $#argv == 0 ) goto arg1err ; if ( 8 == 0 ) goto arg1err set nProtoIters = $argv[1] ; shift ; set nProtoIters = 1000 shift breaksw breaksw end end while ( $#argv != 0 ) while ( 7 != 0 ) set flag = $argv[1] ; shift ; set flag = --distance shift switch ( $flag ) switch ( --distance ) if ( $#argv == 0 ) goto arg1err ; if ( 6 == 0 ) goto arg1err set Distance = $argv[1] ; shift ; set Distance = 50 shift breaksw breaksw end end while ( $#argv != 0 ) while ( 5 != 0 ) set flag = $argv[1] ; shift ; set flag = --no-rescale shift switch ( $flag ) switch ( --no-rescale ) set DoRescale = 0 ; set DoRescale = 0 breaksw breaksw end end while ( $#argv != 0 ) while ( 4 != 0 ) set flag = $argv[1] ; shift ; set flag = --i shift switch ( $flag ) switch ( --i ) if ( $#argv == 0 ) goto arg1err ; if ( 3 == 0 ) goto arg1err set InVol = $argv[1] ; shift ; set InVol = orig.mgz shift breaksw breaksw end end while ( $#argv != 0 ) while ( 2 != 0 ) set flag = $argv[1] ; shift ; set flag = --o shift switch ( $flag ) switch ( --o ) if ( $#argv == 0 ) goto arg1err ; if ( 1 == 0 ) goto arg1err set OutVol = $argv[1] ; shift ; set OutVol = orig_nu.mgz shift breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params if ( $#InVol == 0 ) then if ( 1 == 0 ) then if ( ! -e $InVol ) then if ( ! -e orig.mgz ) then if ( $#OutVol == 0 ) then if ( 1 == 0 ) then goto check_params_return ; goto check_params_return set OutDir = `dirname $OutVol` ; set OutDir = `dirname $OutVol` dirname orig_nu.mgz mkdir -p $OutDir ; mkdir -p . if ( $#LF == 0 ) set LF = $OutDir/mri_nu_correct.mni.log if ( 0 == 0 ) set LF = ./mri_nu_correct.mni.log set LF = ./mri_nu_correct.mni.log if ( -e $LF ) mv $LF $LF.bak if ( -e ./mri_nu_correct.mni.log ) mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak pwd | tee -a $LF pwd tee -a ./mri_nu_correct.mni.log /media/sf_Imagery/FreeSurfer/xx/mri which mri_nu_correct.mni | tee -a $LF which mri_nu_correct.mni tee -a ./mri_nu_correct.mni.log /usr/local/freesurfer/bin/mri_nu_correct.mni echo $cmdargs | tee -a $LF echo --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz tee -a ./mri_nu_correct.mni.log --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz echo "nIters $nIters" | tee -a $LF echo nIters 1 tee -a ./mri_nu_correct.mni.log nIters 1 echo $VERSION | tee -a $LF tee -a ./mri_nu_correct.mni.log echo $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ uname -a | tee -a $LF uname -a tee -a ./mri_nu_correct.mni.log Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4 22:03:48 UTC 2014 i686 i686 i386 GNU/Linux date | tee -a $LF date tee -a ./mri_nu_correct.mni.log Mon Jun 23 15:32:45 EDT 2014 nu_correct -version | tee -a $LF nu_correct -version tee -a ./mri_nu_correct.mni.log Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 if ( ! $#tmpdir ) set tmpdir = $OutDir/tmp.mri_nu_correct.mni.$$ if ( ! 0 ) set tmpdir = ./tmp.mri_nu_correct.mni.1745 set tmpdir = ./tmp.mri_nu_correct.mni.1745 mkdir -p $tmpdir mkdir -p ./tmp.mri_nu_correct.mni.1745 echo "tmpdir is $tmpdir" | tee -a $LF echo tmpdir is ./tmp.mri_nu_correct.mni.1745 tee -a ./mri_nu_correct.mni.log tmpdir is ./tmp.mri_nu_correct.mni.1745 set cmd = ( mri_convert ${HiRes} $InVol $tmpdir/nu0.mnc ) set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc ) if ( $UseFloat ) set cmd = ( $cmd -odt float ) if ( 1 ) set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float ) set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float ) pwd | & tee -a $LF pwd tee -a ./mri_nu_correct.mni.log /media/sf_Imagery/FreeSurfer/xx/mri echo $cmd | & tee -a $LF echo mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float tee -a ./mri_nu_correct.mni.log mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float $cmd | & tee -a $LF mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float tee -a ./mri_nu_correct.mni.log mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=25.00, TE=5.36, TI=0.00, flip angle=30.00 i_ras = (-1, 1.49012e-08, 0) j_ras = (0, 0, -1) k_ras = (-1.30385e-08, 1, -5.96046e-08) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.1745/nu0.mnc... if ( $status ) then if ( 0 ) then @ nthIter = 1 ; @ nthIter = 1 while ( $nthIter < = $nIters ) while ( 1 < = 1 ) echo " " | & tee -a $LF echo tee -a ./mri_nu_correct.mni.log echo "--------------------------------------------------------" | & tee -a $LF echo -------------------------------------------------------- tee -a ./mri_nu_correct.mni.log -------------------------------------------------------- echo "Iteration $nthIter `date`" | & tee -a $LF echo Iteration 1 `date` tee -a ./mri_nu_correct.mni.log date Iteration 1 Mon Jun 23 15:32:49 EDT 2014 @ m = $nthIter - 1 @ m = 1 - 1 set cmd = ( nu_correct -clobber $tmpdir/nu${m}.mnc $tmpdir/nu${nthIter}.mnc ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc ) set cmd = ( $cmd -tmpdir ${tmpdir}/${m}/ ) ; set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ ) if ( $#nProtoIters ) set cmd = ( $cmd -iterations $nProtoIters ) ; if ( 1 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 ) if ( $#StopThresh ) set cmd = ( $cmd -stop $StopThresh ) ; if ( 0 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -stop ) if ( $#Distance ) set cmd = ( $cmd -distance $Distance ) ; if ( 1 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 ) if ( $#FWHM ) set cmd = ( $cmd -fwhm $FWHM ) ; if ( 0 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 -fwhm ) echo $cmd | & tee -a $LF echo nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 tee -a ./mri_nu_correct.mni.log nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 $cmd | & tee -a $LF nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 tee -a ./mri_nu_correct.mni.log [fsuser@xubuntu-VirtualBox:/media/sf_Imagery/FreeSurfer/xx/mri/] [2014-06-23 15:32:49] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.imp Assertion failed at line 827 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) if ( $status ) then if ( 0 ) then rm -f $tmpdir/nu${m}.mnc $tmpdir/nu${m}.imp rm -f ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu0.imp @ nthIter = $nthIter + 1 ; @ nthIter = 1 + 1 echo " " | & tee -a $LF echo tee -a ./mri_nu_correct.mni.log end end while ( $nthIter < = $nIters ) while ( 2 < = 1 ) echo " " | & tee -a $LF echo tee -a ./mri_nu_correct.mni.log echo " " | & tee -a $LF echo tee -a ./mri_nu_correct.mni.log set numnc = $tmpdir/nu$nIters.mnc set numnc = ./tmp.mri_nu_correct.mni.1745/nu1.mnc if ( $DoRescale ) then if ( 0 ) then if ( ! -e $numnc ) then if ( ! -e ./tmp.mri_nu_correct.mni.1745/nu1.mnc ) then echo "ERROR: file $numnc does not exist!" | & tee -a $LF echo ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not exist! tee -a ./mri_nu_correct.mni.log ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not exist! exit 1 ; exit 1 ------------------------------ This transmission, including any attachments, is for the sole use of the intended recipient (s) and may contain information that is confidential, proprietary, legally privileged, or otherwise protected by law from disclosure. Any unauthorized review, use, copying, disclosure, or distribution is prohibited. If you are not the intended recipient, or the person responsible for delivering this to an addressee, you should notify the sender immediately by telephone or by reply e-mail, and destroy all copies of the original message.

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selxavg3-sess error in ==> fast_selxavg3 at 434
by pfannmoelj＠uni-greifswald.de 18 Jul '14

18 Jul '14

Dear Experts, during an fsfast analysis an error occured after selxavg3-sess was executed. The corresponding commands were: mkanalysis-sess -fsd bold -surface self lh -fwhm 0 -event-related -paradigm sensory.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 8 -polyfit 2 -analysis analysis.lh -delay 0 -per-run -force -mcextreg mkcontrast-sess -analysis analysis.lh -contrast stim-v-base -a 1 selxavg3-sess -s ./sessdir -analysis analysis.lh -no-preproc -force The output of selxavg3-sess was: >> >> >> >> >> >> >> sxa3pwd = /.../evaluation >> sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./sessdir -analysis analysis.lh -no-preproc -force >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# sessdir ############################### /.../evaluation/sessdir ------------------------- $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m ------------------------- outtop = /.../evaluation Extension format = nii.gz 1 stim-v-base.mat Excluding 8 points nruns = 1 autostimdur = outanadir = /.../evaluation/sessdir/bold/analysis.lh Excluding 8 points Found 145573/155188 (93.8) voxels in mask Creating Design Matrix ... creation time = 0.008 sec DoMCFit = 1 ntptot = 108, nX = 15, DOF = 93 Saving X matrix to /.../evaluation/sessdir/bold/analysis.lh/Xtmp.mat XCond = 64.7067 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.468819 (t=0.005249) 2 -0.25 -0.252194 (t=0.007053) 3 0 -0.0449419 (t=0.008126) 4 0.25 0.149516 (t=0.00935) 5 0.5 0.319324 (t=0.010795) AR1 Correction M: 0.0749452 1.26122 Computing contrast matrices OLS Beta Pass run 1 t= 0.0 Global Mean Global In-Mask Mean = (0.664951) ??? Error using ==> mrdivide Matrix dimensions must agree. Error in ==> fast_selxavg3 at 434 RescaleFactor = flac0.inorm/gmean; >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Do you have an idea what went wrong? Sincerely yours pfannmoe

2 2

?Sequence for Hippo_subfields
by Kev 17 Jul '14

17 Jul '14

Dear FS experts, I'm in the designing stage of a neuroimaging project on a 3T scanner, and I'm interested in looking at structural information on hippocampus (including subfields). In addition to the MPRAGE or IR-SPGR, is it worth running a specific acquisition sequence geared to get the most out of all the hippocampus structural measures? Thanks and regards, Kev

3 5

Choi2012 convert to FSL MNI152 2mm
by Kathy L. Pearson 10 Jul '14

10 Jul '14

To convert an example Choi2012 file to FSL 2mm space in FreeSurfer 5.2, I have tried both of the mri_vol2vol commands below. The results as shown in freeview are offset by several voxels from the original. Is there a transform or an intermediate step that can make this work -- or a different command? Also, is there a recommended way to extract each individual value (here 1 ... 7) to create separate masks in FSL 2mm space? Thanks for any advice, Kathy Pearson #!/bin/bash input=$FREESURFER_HOME/average/Choi_JNeurophysiol12_MNI152/Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz mri_vol2vol --mov $input --targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o output1.nii.gz --no-save-reg --interp nearest --precision uchar mri_vol2vol --targ $input --mov $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --inv --reg $FREESURFER_HOME/average/mni152.register.dat --o output2.nii.gz --no-save-reg --interp nearest --precision uchar # Compare results freeview $input output1.nii.gz output2.nii.gz&

4 4

problems with Surface-based Interhemispheric Registration
by angela.favaro＠unipd.it 07 Jul '14

07 Jul '14

Hi all, I have a problem with 'Surface-based Interhemispheric Registration' I followed the instructions and all seem to work, but the command: 'surfreg --s $subject --t fsaverage_sym --lh --xhemi' finish with the error below (indeed in the xhemi/label directory, there is no file) What can I do? Thank you for any help! Angela #@# Cortical Parc rh Mon Jun 30 17:44:52 CEST 2014 /Users/angelafavaro/Desktop/risonanze/studyfree/subj024/xhemi/scripts \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subj024/xhemi rh ../surf/rh.sphere.reg /Applications/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot \n No such file or directory mris_ca_label: could not open label file ../label/rh.cortex.label No such file or directory No such file or directory Darwin host-001.homenet.telecomitalia.it 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 recon-all -s subj024/xhemi exited with ERRORS at Mon Jun 30 17:44:52 CEST 2014

4 13

Using the Longitudinal Pipeline
by Alfred Ochs 07 Jul '14

07 Jul '14

Colleagues, We are preparing to perform longitudinal pilot studies a group of subjects and controls under far less than ideal conditions. The initial MRI scans were done clinically on a 1.5T Siemens scanner using the ADNI Siemens scanning protocol. The follow-up scans need to be done on a 3.0T Phillips (research, i.e., gratis) scanner using the ADNI Phillips protocol. Am I correct in assuming that the FreeSurfer longitudinal pipeline will somewhat iron out the inherent segmentation & parcellation differences between MRIs taken on these two machines? Thank you, Alfred Ochs

2 1

mris__label__calc intersect error in longitudinal qcache
by Michael Kranz 07 Jul '14

07 Jul '14

Hi, I'm having trouble figuring out following problem: For one subject (out of 200), I get the following error (this error only persists for the right hemisphere-- left hemisphere works fine for this subject). mris_label_calc intersect /SUBJECTS_DIR/sub2.long.subt/label/rh.cortex.label /SUBJECTS_DIR/subt/label/rh.long.cortex.label /SUBJECTS_DIR/subt/label/rh.long.cortex.label ERROR -11 : mris_label_calc intersect did not work? *subt is base and sub2 is second time point .* Do you guys have any experience with this error and problems that it may have been caused by? I've tried re-running the longitudinal stream from scratch and the error still persists. I've visually checked the images and all segmentations were accurate. Thanks, Mike Kranz

2 1

Re: [Freesurfer] Fw: Problem with uploading Cluster Simulation data
by Douglas Greve 06 Jul '14

06 Jul '14

You should be able to view the map results in freeview just as you would any other map. doug On 6/12/14 12:19 PM, carina(a)van-vlodrop.de wrote: > *Gesendet:* Dienstag, 10. Juni 2014 um 11:18 Uhr > *Von:* "carina(a)van-vlodrop.de" <carina(a)van-vlodrop.de> > *An:* freesurfer(a)nmr.mgh.harvard.edu > *Betreff:* Problem with uploading Cluster Simulation data > Dear freesurfer experts, > we are conducting cortical-thickness analysis using freesurfer-4.4.0 > and the final analysis with qdec. I have a question concerning the > Clusterwise Correction for Multiple Comparison. > Is it correct that I have to visualize the results of the Monte Carlo > Simulation in freeview? > Do I have to upload a special model in freeview before uploading the > Cluster Simulation data? > Yours sincerely, > Carina

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Freesurfer June 2014